jbrowse-plugin-refget-api

This plugin extends a BaseSequenceAdapter to retrieves sequence data from the refget compliant servers

To use this plugin use RefGetAdapter as the adapter type of the assembly names

RefGetAdapter configuration

The RefGetAdapter contains the following configuration options:

serverLocation (optional)

URL of the refget server, the default value is: https://www.ebi.ac.uk/ena/cram/sequence can be changed to any server compliant with the refget schema

sequenceData (mandatory)

A JSON-like object with the following format: sequenceData: { sequenceId: {size:number, name:string}, ... }

sequenceIdType (optional)

By default is an empty string which means that the sequenceId is an md5 checksum

Example query: https://www.ebi.ac.uk/ena/cram/sequence/<md5checksum>?start=NNN&end=NNN

Can be changed to insdc if sequenceId is the INSDC accession or any other value supported by the refget server.

If not empty the query will be modified as the following:

https://www.ebi.ac.uk/ena/cram/sequence/<sequenceIdType>:<md5checksum>?start=NNN&end=NNN

Configuration

a configuration will look like this:

    "assemblies": [
    {
      "name": "assemblyName",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "refseq_track",
        "adapter": {
          "type": "RefGetAdapter",
          "serverLocation": { // optional
            "uri": "https://www.ebi.ac.uk/ena/cram/sequence" //url of the server + /secuence endpoint
          },
          "sequenceIdType": "", // optional
          "sequenceData": {          // mandatory 
            "md5checksum1": {name: chr1, size: 1000000},
            "md5checksum2": {name: chr2, size: 920300},
          }
        }
      }
    }
  ]

To use in @jbrowse/react-linear-genome-view

install it via npm

To use in jbrowse-web

Add to the "plugins" of your JBrowse Web config:

{
  "plugins": [
    {
      "name": "RefGet",
      "url": "https://unpkg.com/jbrowse-plugin-refget-api/dist/jbrowse-plugin-refget-api.umd.production.min.js"
    }
  ]
}

You can also download this file to your local server if you don't want to use a CDN